Bismillahi Al-Rahmani Al-Rahim
Yes, there are consequences if someone habitually omits the sunnah payers associated with the obligatory prayers, the rawatib. In order for a Muslim to be considered upright [`adl], he must fulfill to conditions:
Someone who fails to do both (1a) and (1b) is considered morally corrupt [fisq]. So the consequence of someone who habitually omits the sunnahs associated with the five daily prayers -including witr- is that this is their ruling. Among other things, it is not permissible to pray behind such a person.
[Source: Nail al-ma'arib, 2.476; Hashiyat al-lubadi, p468]
May Allah inspire us to sincerely repent, and may He replace our blameworthy traits with praiseworthy.
And Allah knows best.
Wa al-salamu `alaykum,